search

brainhackorg / global2023

http://brainhack.org/global2023/
MIT License
3 stars 4 forks source link

Launchcontainers: A Python tool for launching containerized analysis on HPC #44

Open yongninglei opened 1 year ago

yongninglei commented 1 year ago

Title

Launchcontainers: A Python tool for launching containerized analysis on HPC

Leaders

Yongning Lei

email: t.lei@bcbl.eu

Collaborators

No response

Brainhack Global 2023 Event

Brainhack Donostia

Project Description

Launchcontainers is a Python-based program built to automatically launch containerlized MRI processing pipelines. This program takes one config.ymal file, one container.json file, and one subject-session-list.txt file as inputs. Using 1 line of bash command, it will automatically send jobs to HPC clusters regarding your computing demands.

This program is well-suited for multi-subject, multi-scan datasets. And it will save a lot of time if you need analysis your entire dataset with different parameters multiple times.

In future versions, we are trying to add more functionality to this repository so that you can launch all the MRI data analysis pipelines such as Heudiconv, fMRIprep, pRF pipelines and etc. Please keep track of this repo and if you have any questions or suggestions, don't hesitate to contact Gari: garikoitz@gmail.com and Tiger: t.lei@bcbl.eu

Link to project repository/sources

https://github.com/garikoitz/launchcontainers

Goals for Brainhack Global

Good first issues

  1. issue one: https://github.com/garikoitz/launchcontainers/issues/28
  2. issue two: https://github.com/garikoitz/launchcontainers/issues/32

Communication channels

https://mattermost.bcbl.eu/bhdonostia/channels/launchcontainer

Skills

Onboarding documentation

https://docs.google.com/document/d/1XMmMpp3w7i2o8wVyHv_kUgoTgYVJ7n-qvgIQilfEBEU/edit?usp=sharing

What will participants learn?

Data to use

I will prepare the converted nifti DWI scan folder in BIDS format and zipped it for use

Number of collaborators

3

Credit to collaborators

Project contributers will be listed in the launchcontainer repo

Image

Launchcontainer logo

Type

documentation coding_methods

Development status

2_releases_existing

Topic

reproducible_scientific_methods

Tools

BIDS

Programming language

Python

Modalities

DWI

Git skills

1_commit_push, 2_branches_PRs

Anything else?

No response

Things to do after the project is submitted and ready to review.

yongninglei commented 1 year ago

Hi @brainhackorg/project-monitors my project is ready!

Remi-Gau commented 1 year ago

hey @yongninglei could you add or tag at least 2 issues in https://github.com/garikoitz/launchcontainers that you want to work on during the hackathon ?

for example have issues that match your "Goals for Brainhack Global" section, so that people who want to help you can at elast say they want to work on this and discuss progress / problems...

yongninglei commented 1 year ago

Hey @Remi-Gau I have add a tag in the repo called for brainhackdonostia 2023 and there are 7 issues ready.

Remi-Gau commented 1 year ago

perfect

yongninglei commented 1 year ago

Hi @Remi-Gau , I attached the launchcontainer logo to this issue just now :DDD maybe it can be added to the web?

Remi-Gau commented 1 year ago

OK testing if relabelling the issue will just reopen a PR with image (that's me being lazy here).

Remi-Gau commented 1 year ago

The image appears in the project page but not as a thumbnail on the listing of projects here: http://brainhack.org/global2023/project/project_44/

Not sure why

likeajumprope commented 1 year ago

quick q: does the project need a localisation label? Such as donostia?

Remi-Gau commented 1 year ago

I think we had them on the previous years but I have not generated the labels

ideally it would be better to use the same labels as we did in the previous years to help do stats across years